Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 5 of 5 for “"Expanded ensemble"”.
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Toward accurate free energy calculations in biomolecular simulation: advances in Markov model reweighting and expanded ensemble method
… into their folded and unfolded conformational ensembles, which are often challenging to obtain from simulations alone due to timescale limitations and force field inaccuracies. This dissertation advances computational tools for molecular design by integrating molecular dynamics (MD) simulations …
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THE USE OF EXPANDED ENSEMBLE FOR THE PREDICTION OF WATER-ORGANIC SOLVENT PARTITION COEFFICIENTS OF SMALL DRUG-LIKE MOLECULES
… sampling complex free energy landscapes. Expanded Ensemble (EE) is an advanced FEP-based technique that enhances sampling and parallelization by allowing the system to explore multiple thermodynamic ensembles during a single simulation. This method has shown considerable flexibility and …
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COMPUTATIONAL APPROACHES FOR PROTEIN FOLDING AND LIGAND BINDING: FROM THERMODYNAMICS TO KINETICS
… these issues, a new approach called multiensemble Markov models (MEMMs) have been developed, in which sampling from biased thermodynamic ensembles can be used to infer states populations and transition rates in unbiased ensembles. In this dissertation, two distinct biophysical problems are …
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Molecular Simulation of Mutation Effects on Protein Folding and Function
… to infer long timescale dynamics from ensembles of short trajectories. These models can be analyzed in a human interpretable way and make physics-based connections to experimental observables. This dissertation describes how we have used MD simulations and MSMs to model protein folding …